R Notebook

library(Seurat)
library(dplyr)
library(tibble)
library(cowplot)

Data loading and processing

General exploratory analysis

U/L branch marker genes

Plot the U and L branch marker genes.

#DE genes between T1T2T3 and T4T5 in the 10x-180831 data.
markers_u_l <- read.table('output/markergenes/180831/markers_10x-180831_upperbranch_lowerbranch_negbinom', sep='\t', header=T)

cannot open file 'output/markergenes/180831/markers_10x-180831_upperbranch_lowerbranch_negbinom': No such file or directoryError in file(file, "rt") : cannot open the connection

How do these genes look in the 180831 data?

And how are they expressed in the Vijay data?

plots <- FeaturePlot(vijay, features=c(as.vector(markers_u$gene)[1:10], as.vector(markers_l$gene)[1:10]), pt.size=1, combine=F)

The following requested variables were not found: RP11-572C15.6

plot_grid(plotlist=plots, ncol=2)

Some U branch markers are not expressed at all (SCD, PLIN4, GDP1). The other U branch markers are expressed in P2 (FABP4), in I1 and I3 and E1-E3.

Seurat integration with 10x-180831 data

Comparison with 10x-180831 data

check marker genes from their paper in 10x-180831 data